MolNFT v1 · #116314 · protein

Structure of HLA-A2:01 with the 11-mer peptide F11V

5D9S · HLA class I histocompatibility antigen, a-2 alpha chain: “Structure of HLA-A2:01 with the 11-mer peptide F11V”. X-ray diffraction, 5 pockets (best druggability 0.66). MolNFT v1 #116314 on GenesisL1: 3D structure, binding sites and…

PDB: 5D9S
Type: protein
Length: 384 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin; 11-mer…
UniProt: P01892, P61769
Pockets: 5 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, a-2 alpha chain	protein	274	27% helix, 41% strand	P01892
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
C	11-mer peptide F11V	protein	11	0% helix, 0% strand	—

Ligands and binding sites

GOL · Glycerol · additive · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	504	0.66	0.78	45	GOL
2	82	0.42	0.79	22	empty
3	84	0.40	0.78	18	empty
4	94	0.34	0.74	19	empty
5	62	0.31	0.76	16	empty

Interfaces

2 interfaces between chains.

A–B · 1290 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 939 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5D9S · Structure of HLA-A2:01 with the 11-mer peptide F11V · the same entry in another collection · chain A against A, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P01892
Every structure of UniProt P61769
Elsewhere: RCSB PDB 5D9S · PDBe 5D9S · UniProt P01892 · UniProt P61769

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